There are several resources, including this question as well as for example problem 5-1 in Kovetz "The Principles of Electromagnetic Theory" which state that the time derivative of a flux can be given: $$ \frac{d}{dt} \int_{S(t)} \vec{A}\cdot \vec{n}ds = \int_{S(t)} (\frac{\partial \vec{A}}{\partial t} + (\nabla \cdot \vec{A})\vec{v} - \nabla \times (\vec{v} \times \vec{A})) \cdot \vec{n}ds. $$
And I have attempted to try and reproduce this result using a method similar to that of the Reynold's Transport Theorem Wikipedia Article.
But I end up with some extra "shear" terms, and I would love to understand where I am going wrong.
The derivation goes as follows. I want to examine the integral of the flux, and so we can rewrite our integral: $$ \int_{S(t)} \vec{A}\cdot\vec{n}ds = \int_{S(t)} \vec{A}(x, y, z, t) \cdot \vec{n} ds = \int_{S(t)} A_x(x(y, z, t), y, z, t) dydz - A_y(x, y(x, z, t), z, t) dxdz + A_z(x, y, z(x, y, t), t) dxdy $$ We can look at this sum of three integrals as three separate integrals, and so we can begin by examining the first one. We first reparameterize from the time-dependent surface of y,z to r,s to get: $$\int_{S(t)} A_x(x(y, z, t), y, z) dydz = \int_{S_0} A_x(x(r, s, t), y(r, s, t), z(r, s, t), t) \lvert\frac{\partial(y, z)}{\partial(r, s)}\rvert drds$$ where $\frac{\partial(y, z)}{\partial(r, s)}$ is the Jacobian of the transformation from y, z to r, s and is a function of time.
We can now differentiate this first term with respect to time to get (employing the product rule and the chain rule for determinants of matrices: $$\frac{d}{dt}\int_{S(t)} A_x(x(r, s, t), y(r, s, t), z(r, s, t), t)\lvert\frac{\partial(y, z)}{\partial(r, s)}\rvert drds =\\ \int_{S_0} \frac{\partial A_x}{\partial t} + \nabla A_x \cdot \vec{v} + A_xtr(\frac{\partial(r, s)}{\partial(y, z)}\frac{\partial(v_y, v_z)}{\partial(r, s)})\lvert\frac{\partial(y, z)}{ \partial(r, s)}\rvert drds$$
Now at a given time, $v_y, v_z$ are only functions of r and s, so we can simplify the trace of the determinant to be just $tr(\frac{\partial(r, s)}{\partial(y, z)}\frac{\partial(v_y, v_z)}{\partial (r, s)}) = \frac{\partial v_y }{\partial y} + \frac{\partial v_z}{\partial z}$
Then, bringing everything together we have $$\frac{d}{dt}\int_{S_0} A_x(x(r, s, t), y(r, s, t), z(r, s, t), t)drds = \int_{S_0} (\frac{\partial A_x}{\partial t} + \nabla A_x \cdot \vec{v} + A_x\frac{\partial v_y }{\partial y} + A_x \frac{\partial v_z}{\partial z})\lvert\frac{\partial(y, z)}{\partial(r, s)}\rvert drds$$
Now, we can identify some like terms, and adopting the notation $\frac{\partial}{\partial x} = \partial_x$, we have by adding and subtracting $\partial_y (A_yv_x)$ and $\partial_z (A_zv_x)$: $$\frac{d}{dt}\int_{S(t)} A_x(x(y, z, t), y, z, t)dydz = \int_{S(t)} \frac{\partial \vec{A_x}}{\partial t} + (\nabla \cdot \vec{A})\vec{v}_x - (\nabla \times (\vec{v} \times \vec{A})))_x + \color{red}{A_y \partial_yv_x + A_z \partial_zv_x}dydz$$
Basically, I am curious if I am doing something wrong, or is it necessary the cumulative shear terms cancel out? (It doesn't seem like that is the case, but open to it). In their derivation Kovetz does not take velocity shear into account, but I imagine these effects would be taken into account in other derivations. Best and thanks in advance!